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Merge branch 'develop' into bias-monitor-django-db
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mfixstsci authored Nov 19, 2024
2 parents a8a8311 + 0aff032 commit f0f5d91
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62 changes: 62 additions & 0 deletions .github/workflows/build.yml
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name: build

on:
release:
types: [ released ]
pull_request:
workflow_dispatch:

defaults:
run:
shell: micromamba-shell {0}

jobs:
build:
uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v1
with:
upload_to_pypi: ${{ (github.event_name == 'release') && (github.event.action == 'released') }}
secrets:
pypi_token: ${{ secrets.PYPI_PASSWORD_STSCI_MAINTAINER }}
freeze:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os:
[ "ubuntu-latest", "macos-latest" ]
python-version:
[ "3.11", "3.12" ]
fail-fast: false
name: freeze versions (Python ${{ matrix.python-version }}, ${{ matrix.os }})
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- uses: mamba-org/setup-micromamba@v1
with:
environment-name: jwql-${{ runner.os }}-py${{ matrix.python-version }}
environment-file: environment.yml
create-args: >-
python=${{ matrix.python-version }}
conda
init-shell: none
generate-run-shell: true
- run: pip install .
- run: pip list
- id: version
uses: mtkennerly/dunamai-action@v1
with:
args: --strict --pattern "default-unprefixed" --style semver
- id: filename
run: echo "filename=jwql_${{ steps.version.outputs.version }}_conda_${{ runner.os }}_${{ runner.arch }}_py${{ matrix.python-version }}.yml" >> $GITHUB_OUTPUT
- run: conda env export --no-build | grep -v "name:" | grep -v "prefix:" > ${{ steps.filename.outputs.filename }}
- run: cat ${{ steps.filename.outputs.filename }}
- uses: actions/upload-artifact@v4
with:
name: ${{ steps.filename.outputs.filename }}
path: ${{ steps.filename.outputs.filename }}
- if: (github.event_name == 'release' && github.event.action == 'released')
uses: svenstaro/upload-release-action@v2
with:
file: ${{ steps.filename.outputs.filename }}


50 changes: 28 additions & 22 deletions .github/workflows/ci.yml
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@@ -1,54 +1,60 @@
name: JWQL CI
name: test

on: [push, pull_request]
on:
push:
pull_request:

concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true

defaults:
run:
shell: bash -l {0}

jobs:
check:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4
with:
python-version: "3.x"
python-version: "3.11"
- run: pip install bandit
- run: bandit ./jwql/ -c .bandit

test:
name: test (Python ${{ matrix.python-version }}, ${{ matrix.os }})
runs-on: ${{ matrix.os }}
strategy:
max-parallel: 5
fail-fast: false
matrix:
os: [ubuntu-latest, macos-latest]
python-version: [3.9, "3.10"]

os: [ "ubuntu-latest", "macos-latest" ]
python-version: [ "3.11", "3.12" ]
fail-fast: false
env:
PYTHONUNBUFFERED: 1
defaults:
run:
shell: micromamba-shell {0}
steps:
- uses: actions/checkout@v4

- uses: mamba-org/provision-with-micromamba@v15
- uses: mamba-org/setup-micromamba@v1
with:
environment-file: ./environment_python_${{ matrix.python-version }}.yml
cache-env: true
cache-downloads: true
environment-name: jwql-${{ runner.os }}-py${{ matrix.python-version }}
environment-file: environment.yml
create-args: >-
python=${{ matrix.python-version }}
init-shell: none
generate-run-shell: true

- run: pip install -e .[test] pytest-xdist

- run: pip install -e .[test]
- run: pip list

- run: conda env export
- run: micromamba env export

- uses: supercharge/[email protected]
- if: runner.os == 'Linux'
uses: supercharge/[email protected]
with:
redis-version: 5.0
if: runner.os == 'Linux'

- run: python -c "import jwql; print('Version ' + jwql.__version__); print('Path ' + jwql.__path__[0])"

- run: pytest jwql/tests/
- run: pytest -n auto jwql/tests/
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -19,3 +19,4 @@ jwql/website/apps/jwql/static/filesystem
jwql/website/apps/jwql/static/outputs
jwql/website/apps/jwql/static/preview_images
jwql/website/apps/jwql/static/thumbnails
jwql-current.yml
8 changes: 3 additions & 5 deletions .readthedocs.yaml
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Expand Up @@ -12,10 +12,7 @@ version: 2
build:
os: ubuntu-22.04
tools:
python: "3.9"
jobs:
post_install:
- pip install sqlalchemy==1.4.46
python: "3.11"

# Build documentation in the docs/ directory with Sphinx
sphinx:
Expand All @@ -27,6 +24,7 @@ sphinx:
# Optionally declare the Python requirements required to build your docs
python:
install:
- requirements: rtd_requirements.txt
- method: pip
path: .
extra_requirements:
- docs
133 changes: 133 additions & 0 deletions CHANGES.rst
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@@ -1,5 +1,138 @@
## What's Changed

1.2.11 (2024-08-26)
===================

Web Application
~~~~~~~~~~~~~~~
- Customize colorbar location and size based on aperture size by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1592
- Add keyword to specify program IDs for preview image creation by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1602
- Adjust view image and view exposure to allow for larger preview images by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1600
- filter thumbnails by filter/pupil/grating by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1623
- Add Image and Exposure level Comments by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1624
- Update NRS TA Monitor Plotting by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1633
- Fix readnoise monitor plot y range by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1634

Project & API Documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Update Bokeh `filter` Keyword in NRS TA Monitors by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1620
- Switch dark monitor to use django models by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1493
- Fix log cleanup script by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1628
- Fix missing data in readnoise monitor plots by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1631
- filename_parser() no longer raises an exception for unrecognized files by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1614


1.2.10 (2024-07-10)
===================

Duplicate of 1.2.9, caused by changes to versioning conflicts with pypi.


1.2.9 (2024-07-10)
==================

Web Application
~~~~~~~~~~~~~~~
- Add Download CSV button to query page by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1561
- show file anomalies on exposure group page by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1564
- create generic error page to handle exceptions in views. by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1549

Project & API Documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~~
- final model define for faking by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1544
- Update Redis Package Names in Environment Files by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1546
- [SCSB-145] require Python 3.10 by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1515
- debug false by default by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1550
- Update NIRSpec TA Monitors to use Django DB Models by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1499
- Update NIRSpec TA Models by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1565
- Remove codecov.yml by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1588
- Remove filename parser test over filesystem by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1586
- Update remote to upstream in pull_jwql_branch.sh by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1591
- Add Dependencies for Servers in `pyproject.toml` by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1568
- fix release upload step condition to match workflow trigger by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1593
- fix environment freeze workflow not picking up tag by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1594
- fix version matching pattern by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1595
- updating freeze matrix to include linux, mac and python 3.12 by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1596
- Remove P750L from list of NIRSpec filters by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1598
- [build] fix `runs-on:` and update build filename for easier parsing by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1599
- upload to PyPI on release by @zacharyburnett in https://github.com/spacetelescope/jwql/pull/1601
- Updating jwst_reffiles version number by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1606
- Remove old presentations from repo by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1607
- Num results fix by @BradleySappington in https://github.com/spacetelescope/jwql/pull/1608
- Add Environment Update Script by @mfixstsci in https://github.com/spacetelescope/jwql/pull/1609
- Add new NIRISS AMI-related suffixes by @bhilbert4 in https://github.com/spacetelescope/jwql/pull/1613


1.2.8 (2024-04-18)
==================

Web Application
~~~~~~~~~~~~~~~

Project & API Documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~~
- final model define for faking by @BradleySappington


1.2.7 (2024-04-18)
==================

Web Application
~~~~~~~~~~~~~~~

Project & API Documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Import monitor models by @bhilbert4


1.2.6 (2024-04-15)
==================

Web Application
~~~~~~~~~~~~~~~
- Update NIRCam Background Monitor plots to handle new Claw Monitor columns by @bsunnquist

Project & API Documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~~
- add default to read_patt_num by @BradleySappington
- migration work for next RC by @BradleySappington
- Fix database empty fields by @BradleySappington


1.2.5 (2024-03-19)
==================

Web Application
~~~~~~~~~~~~~~~
- Fix Bokeh `file_html` Call by @mfixstsci
- Update Bad Pix Exclude Line by @mfixstsci
- Interactive preview image - updates for Bokeh 3 by @bhilbert4

Project & API Documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Allow creation of pngs from 3D and 4D arrays by @bhilbert4
- Add max length to charfield by @BradleySappington
- Header fix by @BradleySappington


1.2.4 (2024-03-11)
==================

Web Application
~~~~~~~~~~~~~~~
- Fix Broken Dashboard - ReImplement Anomaly Dash @BradleySappington
- Add more info to image- and exposure-level pages @bhilbert4

Project & API Documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~~
- create pull_jwql_branch.sh by @BradleySappington
- Claw monitor migrate by @york-stsci
- Update readnoise monitor to use django database models by @york-stsci
- Migration to django management by @york-stsci
- Get subarray lists from datamodels schema by @bhilbert4
- Retrieve program number and category efficiently by @bhilbert4


1.2.3 (2024-01-26)
==================

Expand Down
6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -44,7 +44,7 @@ Getting `jwql` up and running on your own computer requires four steps, detailed

### Prerequisites

It is highly suggested that contributors have a working installation of `anaconda` or `miniconda` for Python 3.9+. Downloads and installation instructions are available here:
It is highly suggested that contributors have a working installation of `anaconda` or `miniconda` for Python 3.10+. Downloads and installation instructions are available here:

- [Miniconda](https://conda.io/miniconda.html)
- [Anaconda](https://www.continuum.io/downloads)
Expand Down Expand Up @@ -86,13 +86,13 @@ source activate base/root
Lastly, create the `jwql` environment via one of the `environment.yml` files (currently `environment_python_3.9.yml`, for python 3.9, and `environment_python_3.10.yml`, for python 3.10, are supported by `jwql`):

```
conda env create -f environment_python_3.9.yml
conda env create -f environment_python_3.10.yml
```

or

```
conda env create -f environment_python_3.10.yml
conda env create -f environment_python_3.11.yml
```

### Configuration File
Expand Down
36 changes: 0 additions & 36 deletions codecov.yml

This file was deleted.

3 changes: 3 additions & 0 deletions environment.yml
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@@ -0,0 +1,3 @@
dependencies:
- firefox
- python
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